tbuckley/cabot-search huggingface dataset:
Abstract 2944: Rapid and accurate variant calling of FFPE samples with the Genexus System
Authors: Iris Casuga, Frances Chan, Milton Huynh, Gregory R. Govoni, Kayla Zochowski, Thilanka Jayaweera, Janice Au-Young
Journal: Cancer Research (2022)

Abstract Next-Generation Sequencing technology has enhanced oncology research by enabling the detection of all cancer related variants into one assay for research and drug discovery programs. The Oncomine࣪ Comprehensive Assay v3, a pan-cancer panel, used with the Ion Torrent࣪ Genexus࣪ System allows for formalin-fixed paraffin embedded (FFPE) samples to be examined across 161 unique genes in an automated sample to result workflow in 30hrs. This study demonstrates ≥ 95% Sensitivity and PPV for detecting SNV, Indel, and Copy Number variants of clinical FFPE samples along with fusions. When tested using analytical controls, the Genexus System achieves ≥ 98% Sensitivity for hotspot variants, ≥ 95% for de novo variants, and 100% Sensitivity for fusion variants. The Ion Torrent࣪ Genexus࣪ System is fully automated and consists of two software linked instruments, the Ion Torrent࣪ Genexus࣪ Purification System and the Ion Torrent࣪ Genexus࣪ Integrated Sequencer. For this study, the purification system was used to sequentially extract and quantify DNA &amp; RNA samples from human colon and lung FFPE tumor tissue. The purification instrument provides minimal hands-on-time, ease of use and compatibility with the integrated sequencer. It extracts and quantifies the nucleic acids, records the quantitation values and transfers the nucleic acids to an output plate. The plate is transferred from the purification instrument directly to the sequencer for sample dilution, library preparation, and sequencing using the Oncomine࣪ Comprehensive Assay v3 panel. Variant calling analysis of the DNA &amp; RNA pairs is completed immediately following sequencing. Results show that the variants are detected reproducibly with ≥ 95% Sensitivity and PPV when compared to the Ion GeneStudio࣪ S5 System as an orthogonal method. All variants in the report were correct with p-values ≤ 10-5. Additionally, a subset of the extracted samples was evaluated using Sanger Sequencing to verify hotspot mutations found in samples sequenced on both the Genexus࣪ System and GeneStudio࣪ S5 System. Results show that all expected hotspot variants were detected. In summary, the Ion Torrent࣪ Genexus࣪ System is a reliable and fast turnaround solution for sample-to-variant calling results. When used with the Oncomine࣪ Comprehensive Assay v3 panel, the system provides accurate identification of tumor markers for oncology research. Citation Format: Iris Casuga, Frances Chan, Milton Huynh, Gregory R. Govoni, Kayla Zochowski, Thilanka Jayaweera, Janice Au-Young. Rapid and accurate variant calling of FFPE samples with the Genexus System [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2944.
Abstract 3281: DNMT targeting enhances vulnerability of glioblastoma cells to MNK inhibition
Authors: Candice Mazewski, Frank Eckerdt, Aneta Baran, Mariafausta Fischietti, Purav P. Vagadia, Ricardo E. Perez, Charles D. James, Gary E. Schiltz, Leonidas C. Platanias
Journal: Cancer Research (2022)

Abstract Many factors complicate therapeutic strategies for glioblastoma (GBM), including the existence of the blood brain barrier and a heterogenous population of difficult to treat glioma stem cells. Innovative strategies targeting novel pathways alone or in combination are needed for sustainable therapeutic improvements. The MAPK pathway has been implicated in many cancers. MAPK interacting kinases (MNK1 and MNK2) are downstream of MAPKs and phosphorylate the eukaryotic translation initiation factor 4E (eIF4E), a protein involved in translation of oncogenic mRNAs. We have previously established pharmacological MNK inhibition as a promising strategy for GBM. However, most currently available MNK inhibitors lack specificity and exhibit off-target effects. We developed novel selective MNK inhibitors that show MNK inhibition specificity in GBM established cell lines as well as patient-derived cell lines propagated under stem cell permissive conditions as 3-D neurospheres. MNK inhibitors reduced cell viability and neurosphere growth. Our previous work with MNK inhibitors showed involvement in negative feedback loops activated with treatment of other pharmacological agents, so we conducted a high-throughput screening to identify potential targets for combination treatment. One of the top hits was a DNA methyltransferase (DNMT) inhibitor that enhanced MNK inhibitor antineoplastic effects in GBM cells. Dual MNK and DNMT inhibition synergistically reduced neurosphere growth in 3-D glioma stem-like cells. The combination promoted apoptosis in the mesenchymal glioma stem-like cells as shown through flow cytometry and increased expression of cleaved PARP, cleaved caspase 3, and Bax. Also, DNMT targeting enhanced the viability reduction effects of siRNA mediated MNK1 knockdown in GBM cells. This combination of our novel MNK inhibitor with DNMT inhibition elicited antineoplastic benefits in both 2-D cultures and 3-D glioma stem cell-like populations, demonstrating a potential novel therapeutic strategy in GBM. Citation Format: Candice Mazewski, Frank Eckerdt, Aneta Baran, Mariafausta Fischietti, Purav P. Vagadia, Ricardo E. Perez, Charles D. James, Gary E. Schiltz, Leonidas C. Platanias. DNMT targeting enhances vulnerability of glioblastoma cells to MNK inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3281.
Abstract 5529: <i>In vivo</i> efficacy evaluation of ASC61, an oral PD-L1 inhibitor, in two tumor mouse models
Authors: Jinzi J. Wu, Handan He
Journal: Cancer Research (2022)

Abstract Background: ASC61 is an oral inhibitor prodrug of programmed cell death-ligand 1 (PD-L1). ASC61 is converted to its pharmacologically active metabolite ASC61-A in the plasma. In vitro studies showed that ASC61-A could activate PD-L1 dimerization and membrane PD-L1 protein internalization, interfere PD-1/PD-L1 interaction and enhance T-cell activation. Here we report the in vivo efficacy of ASC61 in two tumor mouse models. ASC61 was found to have the best antitumor activity among all test drugs in the syngeneic tumor mouse model, BALB/c mice bearing CT-26-hPD-L1 tumors. Then a humanized mouse model, PD-1/PD-L1 dKI HuGEMM bearing hPD-L1 MC38 tumor, was used to further validate the therapeutic efficacy of ASC61. Methods: In the BALB/c mouse model, mice were inoculated subcutaneously with CT-26-hPD-L1 cells. When the average tumor volume reached approximately 69 mm3, mice were randomly assigned and treated twice a day (BID) with vehicle, reference drug (Atezolizumab), ASC61, GLC01-589 or GLC01-633 for 19 days. In the PD-1/PD-L1 dKI HuGEMM mouse model, MC38 hPD-L1 cells were subcutaneously inoculated in the right rear flank region of mice. Once the mean tumor size reached approximately 78.3 mm3, mice were randomized and treated BID for 16 days with vehicle, Atezolizumab, ASC61 (50 or 100 mg/kg). In both models, body weights and tumor volumes were measured regularly, and tumor growth inhibitions (TGI) of different groups were compared. Results: All mice showed a gradually increase in body weight during the study and no significant difference of body weight or body weight change was found among different groups in both mouse models. In the BALB/c mouse model, ASC61 50 mg/kg showed significantly inhibitory effects on the tumor growth with the best TGI value of 52.9% (p &amp;lt; 0.05) on Day 19, even better than that of the reference drug (40.77%). In the PD-1/PD-L1 dKI HuGEMM mouse model, Group 2 to 4 showed TGI values of 69.62%, 33.62% and 63.15% on Day 16, respectively. Atezolizumab 5 mg/kg BIW and ASC61 100 mg/kg BID produced similar significant antitumor efficacies (both p &amp;lt; 0.001). Survival analysis showed significant differences between Group 1 and Group 2 to 4 (p = 0.0002, 0.0338 and 0.0027, respectively). Conclusion: Results of this study show that ASC61 is well tolerated in both mouse models, and ASC61 has comparable antitumor efficacies as the FDA-approved PD-L1 antibody, Atezolizumab. ASC61 is an oral PD-L1 inhibitor, and thus will have better patient compliance than injective PD-1/PD-L1 antibody. ASC61 first in human clinical trial will begin soon. Citation Format: Jinzi J. Wu, Handan He. In vivo efficacy evaluation of ASC61, an oral PD-L1 inhibitor, in two tumor mouse models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5529.
Abstract 3836: Mapping the interactome of the endogenous metalloproteinase inhibitor TIMP2 using extracellular proximity labeling (ePL)
Authors: David Peeney, Sadeechya Gurung, Yueqin Liu, Carolyn Lazaroff, Christopher Richie, William G. Stetler-Stevenson
Journal: Cancer Research (2022)

Abstract Tissue inhibitors of metalloproteinases (TIMPs) are a family of endogenous proteins that were initially defined by their ability to inhibit the enzymatic activity of matrix metalloproteinases (MMPs), the major mediators of ECM breakdown and turnover. TIMPs are important regulators of ECM structure, function and homeostasis. Since their original discovery, additional MMP-independent functions have been attributed to TIMP family members leading to their designation as multifunctional proteins with discrete functional domains. TIMP2 is a unique family member, with a broad expression profile that is expressed in both normal and diseased tissues, even in those with minimal metalloproteinase activity. Understanding the functional transformation of matrisome regulators, like TIMP-2, during the dynamic evolution of tissue microenvironments associated with disease progression is essential to the development of ECM targeted therapeutics. This knowledge may also garner understanding of therapeutic resistance and the failure of conventional and next-generation cancer therapies. Interactome studies are predominantly performed in non-living systems, and very rarely performed in complex culture systems such as 3D spheroids/co-cultures. To investigate the TIMP-2 interactome in complex biological systems we recently developed carboxyl- and amino-terminal fusion genes of TIMP-2 with the promiscuous biotinylating peptides BioID2 and TurboID. Packaged for retroviral delivery, this system gives us great flexibility in assessing the TIMP-2 interactome in simple versus complex 3D co-culture systems. We show, for the first time, that conditions can be optimized to support proximity labeling reactions in the extracellular milieu, representing an important technical resource for extracellular matrix biologists. Using this method, we identify novel interacting partners for TIMP-2 that provide insight into the tissue-specific actions of this protein in both healthy and diseased tissues. Citation Format: David Peeney, Sadeechya Gurung, Yueqin Liu, Carolyn Lazaroff, Christopher Richie, William G. Stetler-Stevenson. Mapping the interactome of the endogenous metalloproteinase inhibitor TIMP2 using extracellular proximity labeling (ePL) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3836.
Abstract 2504: Next generation sequencing identifies novel potential biomarkers for DICER1 syndrome
Authors: Mona K. Wu, Raphael D. Lopez, Mikako Warren, Rachana Shah, Paolo Neviani, James F. Amatruda
Journal: Cancer Research (2022)

Abstract MicroRNAs (miRNAs) are small RNA molecules that play a critical role in regulating gene expression. The DICER1 enzyme is a key component of the microRNA biogenesis pathway. Reflecting this central role, patients who inherit or acquire mutations in the DICER1 gene have an increased risk of developing a spectrum of benign and malignant tumors —thereby earning the recognition as a pediatric cancer predisposition syndrome known as DICER1 syndrome (OMIM 601200). DICER1 syndrome is definitively diagnosed by DNA sequencing demonstrating presence of a loss of function mutation on one copy of DICER1 plus a “hotspot” mutation on the other copy of DICER1. As tumor and germline DNA sequencing can pose logistical and/or cost difficulties, a complementary diagnostic method based on marker expression is valuable for both diagnostics and surveillance. Biomarkers that are candidate therapeutic targets are also appealing as these may offer a more tailored approach for therapy. As there are no approved biomarkers for identification of DICER1-associated tumors, we performed RNAseq and miRNAseq in an engineered murine mesenchymal cell model that incorporates a specific DICER1 hotspot mutation to identify candidates. We validated candidate biomarkers at the RNA (Eya2, Vipr1, miR-139-3p, and miR-30d-3p) and protein (Eya2, and Vipr1) levels in vitro, to provide proof of principle data for their eventual clinical utility. The miRNA candidate biomarkers levels were evaluated in both total and small extracellular vesicle-enriched fractions. These novel data pave the way for additional tools for diagnosis and surveillance in patients with DICER1 syndrome. Citation Format: Mona K. Wu, Raphael D. Lopez, Mikako Warren, Rachana Shah, Paolo Neviani, James F. Amatruda. Next generation sequencing identifies novel potential biomarkers for DICER1 syndrome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2504.
Abstract 860: Identifying mechanisms associated with slow proliferation of BAP1 mutant uveal melanoma cells
Authors: Vivian Chua, Usman Baqai, Timothy J. Purwin, Angela Jeon, Anna Han, Andrew Aplin
Journal: Cancer Research (2022)

Abstract Uveal melanoma (UM) is the deadliest form of eye cancer in adults. Primary tumors in the uveal tract are often treated successfully by enucleation or radiotherapy but 50% of cases develop metastases which occur primarily in the liver. Patients diagnosed with metastatic UM usually have a poor prognosis with a short median survival of 5-18 months due to the lack of effective treatment options. Metastatic UM responds poorly to many therapeutic options. Inactivating mutations in BRCA1-associated protein 1 (BAP1), a tumor suppressor gene and de-ubiquitinating (DUB) enzyme, have been reported in &amp;gt;80% metastasizing UM and thus are associated with elevated risks of UM metastasis. However, the role of BAP1 in UM metastasis is unclear. Interestingly, silencing of BAP1 in UM cell lines was shown to inhibit UM cell proliferation and cell cycle progression. Consistent with this finding, we show that BAP1-deficient or BAP1 mutant UM cells proliferated slower than BAP1 wild-type (WT) cell lines. Re-expression of BAP1 in a BAP1-deficient or mutant UM cell line, MP65, also increased the proliferation rate of cells. Analysis of reverse phase protein array (RPPA) identified that phosphorylation of the S6 ribosomal protein is elevated in BAP1 proficient cells. Re-expression of BAP1 WT also increased phosphorylation of S6 and its upstream regulator, p70S6K1. Additionally, BAP1 mutant UM cells were more viable compared to isogenic cells expressing BAP1 WT in response to amino acid deprivation. These findings suggest that loss of BAP1 is associated with better survival under environmental stress, a critical step during metastasis. Positivity for pS6 was detected in all metastatic UM specimen tested regardless of BAP1 status. This suggests a role of the tumor microenvironment in regulating pS6 levels in UM cells at the metastatic site. Our findings show BAP1-dependent regulation of UM cell proliferation and response to stress, and uncover S6 and its associated pathway as an opportunity for therapeutic target in BAP1 mutant UM. Citation Format: Vivian Chua, Usman Baqai, Timothy J. Purwin, Angela Jeon, Anna Han, Andrew Aplin. Identifying mechanisms associated with slow proliferation of BAP1 mutant uveal melanoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 860.
Abstract 244: Limiting metastatic breast cancer progression by targeting MK2 stromal signaling
Authors: Renata Ramalho Oliveira, Douglas V. Faget, Xianmin Luo, Jiayu Ye, Joseph B. Monahan, Sheila A. Stewart
Journal: Cancer Research (2022)

Abstract Breast cancer is now the most common cancer among women in the US and metastasis to distant organs is the major cause of death in these patients. Among metastatic sites, bone is the most frequent destination of breast cancer metastasis and once the disease is found in the bone, it is often refractory to standard therapy. In addition, bone metastasis is associated with significant skeletal related events that greatly impact quality of life. Thus, there is a significant need to develop novel therapies that extend survival and improve quality of life. Previously we found that MK2 inhibition (MK2i) limits metastatic growth by targeting the tumor stromal compartment. To determine which stromal cells are targeted by MK2i we isolated stromal cells from within a metastatic bone lesion and carried out single cell RNA sequencing (scRNA-Seq). Using this approach, we found numerous gene expression changes in both the immune (CD45+) and non-immune (CD45-) populations upon MK2i. Indeed, we found significant numbers of p16+ senescent fibroblasts were present inside the metastatic lesion. We also found vascular cancer-associated fibroblasts (vCAF) and matrix CAFs (mCAF) inside the metastatic lesion suggesting that CAFs are not limited to primary disease. Numerous changes in gene expression in CD45+ cells were also observed, and these changes are being used to identify viable immunotherapies to deploy in our model. Finally, we are using conditional MK2 mice to establish the cell type targeted by MK2i. Our data demonstrate that MK2i is as effective as chemotherapy at limiting metastatic progression and our approach to leverage the scRNA-Seq data may allow us to optimize MK2i therapy to improve patient outcomes and quality of life. Citation Format: Renata Ramalho Oliveira, Douglas V. Faget, Xianmin Luo, Jiayu Ye, Joseph B. Monahan, Sheila A. Stewart. Limiting metastatic breast cancer progression by targeting MK2 stromal signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 244.
Activation of Hedgehog signaling by the oncogenic RELA fusion reveals a primary cilia-dependent vulnerability in supratentorial ependymoma
Authors: Taciani de Almeida Magalhães, Gustavo Alencastro Veiga Cruzeiro, Graziella Ribeiro de Sousa, Bernhard Englinger, Luis Fernando Peinado Nagano, Mathew Ancliffe, Keteryne Rodrigues da Silva, Li Jiang, Johannes Gojo, Yulu Cherry Liu, Brooke Carline, Mani Kuchibhotla, Fabiano Pinto Saggioro, Suely Kazue Nagahashi Marie, Sueli Mieko Oba-Shinjo, José Andres Yunes, Rosane Gomes de Paula Queiroz, Carlos Alberto Scrideli, Raelene Endersby, Mariella G Filbin, Kleiton Silva Borges, Adrian Salic, Luiz Gonzaga Tone, Elvis Terci Valera
Journal: Neuro-Oncology (2022)

BackgroundSupratentorial RELA fusion (ST-RELA) ependymomas (EPNs) are resistant tumors without an approved chemotherapeutic treatment. Unfortunately, the molecular mechanisms that lead to chemoresistance traits of ST-RELA remain elusive. The aim of this study was to assess RELA fusion-dependent signaling modules, specifically the role of the Hedgehog (Hh) pathway as a novel targetable vulnerability in ST-RELA.
Abstract LB536: Newly established CAR-T target antigen luciferase reporter cell lines facilitate CAR-T development
Authors: John Foulke, Brian Della Fera, Luping Chen, Fang Tian
Journal: Cancer Research (2022)

Abstract Adoptive T cell therapy is a type of immunotherapy in which T cells are genetically modified to fight tumors. It has emerged as an exciting new approach for cancer treatment. Chimeric antigen receptor (CAR)-T cells have displayed remarkable efficacy in treating malignant cancers, particularly liquid tumors. CAR-T cells have proven to be a new type of ’living’ therapeutic by harnessing the patients' immune system to recognize specific tumor associated antigens and redirect the engineered T cells to more specifically target tumor cells. A large number of research efforts have been put into developing new CAR structures to increase the scope of targeted cancers and anti-tumor efficacy. Evaluating the biofunction of CAR-T cells in vitro often involves a series of labor-intensive co-culture experiments and immunoassays. Reproducibility also remains a challenge during the validation of new CAR-T cells due to donor-to-donor variation and other factors. In this study, we present a panel of luciferase reporter tumor cell lines that can be utilized to examine the function of CAR-T cells. The panel of selected human tumor cell lines naturally express high levels of CAR-T target antigens on cell surface, such as CD19, CD20 and Her2. After introduction of a Lenti-LUC2 luciferase reporter into the parental cell lines, single cell cloning was performed to isolate stable clones with high luciferase expression. To verify the performance of the target Luciferase reporter cell lines, we used commercially available CAR-T cells expressing CD19, CD20, HER2 and empty vector-transduced T cells as controls in co-culture experiments. The cytotoxicity of the CAR-T cells against target tumor cells was measured using both a luciferase assay and the xCELLigence potency assay. Our results demonstrate that the luciferase reporter system is a relatively simple, robust, and highly sensitive means to measure biological processes. The luciferase reporter cell lines provide an advantage in measuring target cell killing without having to use radioactive 51Cr release assay or pre-labeling the cells in CAR-T functional evaluation. In addition, these reporter cell lines were characterized and authenticated using cell morphology, growth kinetics, and STR analysis. The expression stability of both the target antigen and luciferase was verified by comparing the low passage and the high passage reporter cells. In summary, the well-characterized CAR-T target antigen luciferase reporter cell lines from ATCC provide excellent tools for studying CAR-T biofunction and validating new CAR-T agents for cancer immunotherapy. Citation Format: John Foulke, Brian Della Fera, Luping Chen, Fang Tian. Newly established CAR-T target antigen luciferase reporter cell lines facilitate CAR-T development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB536.